An HD ("hierarchical deterministic") wallet generates keys from the seed in a repeatable way. When you back up the seed, you are backing up all the keys that the wallet will ever generate. Note that backing up the seed does not back up imported keys.
Electrum servers do not hold your keys. They are generated from the seed (unless they are imported). You are backing up the seed, not a passphrase.
No. They are stored on your hard drive (don't know about Hive). If you find the Electrum and MultiBit data folders, you will find wallet files. The wallet files contain your private keys and seed. They will be encrypted if you set a password on your wallet. You don't need QR codes for backup at all. They are not necessary.
Follow the wallet's instructions. If the wallet does not have a method for backing up the seed and/or keys, then don't use it.